Genetical research最新文献

A hitch-hiking guide to the genome: a commentary on 'The hitch-hiking effect of a favourable gene' by John Maynard Smith and John Haigh. 基因组搭便车指南:约翰·梅纳德·史密斯和约翰·黑格对“有利基因的搭便车效应”的评论。

Genetical research Pub Date : 2007-12-01 DOI: 10.1017/S0016672308009580

B. Charlesworth

引用次数: 19

Unravelling the evolutionary advantage of sex: a commentary on 'Mutation-selection balance and the evolutionary advantage of sex and recombination' by Brian Charlesworth. 解开性的进化优势:布莱恩·查尔斯沃思对“突变选择平衡和性与重组的进化优势”的评论。

Genetical research Pub Date : 2007-12-01 DOI: 10.1017/S001667230800966X

S. Otto

引用次数: 13

Proper experimental design and sound statistical inference win every time: a commentary on 'Statistical design and the analysis of gene expression microarray data' by M. Kathleen Kerr and Gary A. Churchill. 正确的实验设计和合理的统计推断每次都能胜出:凯瑟琳·克尔和加里·丘吉尔对“基因表达微阵列数据的统计设计和分析”的评论。

Genetical research Pub Date : 2007-12-01 DOI: 10.1017/S0016672308009725

R. Doerge

引用次数: 1

Wild populations are smaller than we think: a commentary on 'Effective population size/adult population size ratios in wildlife: a review' by Richard Frankham. 野生种群比我们想象的要小:理查德·弗兰克汉姆对《野生动物的有效种群规模/成年种群规模比率:综述》的评论。

Genetical research Pub Date : 2007-12-01 DOI: 10.1017/S0016672308009701

T. Mackay

{"title":"Wild populations are smaller than we think: a commentary on 'Effective population size/adult population size ratios in wildlife: a review' by Richard Frankham.","authors":"T. Mackay","doi":"10.1017/S0016672308009701","DOIUrl":"https://doi.org/10.1017/S0016672308009701","url":null,"abstract":"where H0 is the heterozygosity of the population before the bottleneck, Ht is the heterozygosity after t generations of maintenance with 2N individuals and F is the inbreeding coefficient (Falconer & Mackay, 1996). Clearly heterozygosity decreases, and inbreeding increases, as N decreases ; and these effects accumulate over time. However, no real population fits the ideal model on which this theory is based, which includes self-fertilization in random amounts. The concept of effective population size enables us to utilize this expression by replacing the N in the equation with Ne, where Ne, the effective population size, is the number of individuals that would give rise to the same variance in gene frequency or rate of inbreeding as an ideal population of that size (Falconer & Mackay, 1996). Major departures from the ideal population model that affect Ne are unequal numbers of males and females, unequal numbers of individuals in different generations, non-random distribution of family size, and overlapping generations. Analytical expressions relating the census size of the population (N) to the effective population size have been derived for each of these cases (Frankham, 1995; Falconer & Mackay, 1996) ; under most scenarios Ne<N. Knowledge of the ratio ofNe toN is critical in wildlife populations and particularly endangered species, if we are to predict the rate of inbreeding and loss of heterozygosity. In this meta-analysis, Frankham (1995) synthesizes data from 192 estimates of Ne/N from 102 species. The estimates of Ne/N from insects, molluscs, amphibians, reptiles, birds, mammals and plants ranged from 10x6 in Pacific oysters to 0.99 in humans, and averaged 0.34 overall. However, these studies differed in whether they included fluctuating population size, variable family size and/or different numbers of males and females – less than one-third of the studies included all three of these factors. In addition, different measures of census size were used as the denominator. Some studies utilized the total census size (NT, the total number of adults and juveniles), some the number of adults (NA, the number of breeding plus senescent adults), while others counted only the number of breeding individuals (NB). Finally, both genetic and demographic methods were used. Frankham (1995) capitalized on this variability to perform stepwise regression analyses in order to determine the major variables affecting Ne/N. The significant variables, in decreasing order of importance, were fluctuating population size, variable family size, method of determining census number, taxonomic group, and the sex ratio. The most striking conclusion was that the comprehensive estimates of Ne/N in wild species, including all variables, were of the order of 10%. This is much smaller than had been thought previously and a cause for concern in terms of long-term population viability. This influential review stimulated many studies estimating Ne/N in a wide variety of wild specie","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"38 1","pages":"489"},"PeriodicalIF":0.0,"publicationDate":"2007-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75552551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

The Hill-Robertson effect is a consequence of interplay between linkage, selection and drift: a commentary on 'The effect of linkage on limits to artificial selection' by W. G. Hill and A. Robertson. 希尔-罗伯逊效应是连锁、选择和漂移之间相互作用的结果:w·g·希尔和a·罗伯逊对“连锁对人工选择限制的影响”的评论。

Genetical research Pub Date : 2007-12-01 DOI: 10.1017/S0016672308009506

Z. Zeng

引用次数: 0

Hybrid dysgenesis: from darkness into light: a commentary on 'Hybrid dysgenesis in Drosophila melanogaster: rules of inheritance of female sterility' by William R. Engels. 杂交发育不良:从黑暗到光明:对威廉·r·恩格斯的《黑胃果蝇的杂交发育不良:雌性不育的遗传规则》的评论。

Genetical research Pub Date : 2007-12-01 DOI: 10.1017/S0016672308009609

D. Finnegan

{"title":"Hybrid dysgenesis: from darkness into light: a commentary on 'Hybrid dysgenesis in Drosophila melanogaster: rules of inheritance of female sterility' by William R. Engels.","authors":"D. Finnegan","doi":"10.1017/S0016672308009609","DOIUrl":"https://doi.org/10.1017/S0016672308009609","url":null,"abstract":"One of the many striking insights to have come from sequencing complete genomes is the realization that transposable elements make up a large proportion of the DNA of most eukaryotes. These elements are far from minor players on the genomic stage. They have had a major role in genome evolution and are a significant source of genome instability. Transposable elements are driven to high copy number by transposition, but their activity is difficult to study experimentally as most copies are defective, and the few that are transpositionally competent move infrequently. This is good for the host organism, but not for anyone wanting to study them. A small number of transposable elements in Drosophila transpose at high levels in the progeny of particular crosses. This results in genetic instability manifest by reduced fertility of one or both sexes and a high frequency of germ line mutations, a phenomenon known as hybrid dysgenesis (Kidwell, 1977). P–M hybrid dysgenesis, for example, is seen when males of a P-type strain are crossed with females of an M-type strain, but not in the progeny of the reciprocal cross. At the heart of hybrid dysgenesis is a breakdown in the control of transposition. This was not immediately apparent and for several years hybrid dysgenesis was regarded as a strange phenomenon that appeared to run counter to accepted ‘ rules ’ of genetics. Bill Engels was one of the first to address this, and his analysis of the genetic basis for the difference between P and M strains established a paradigm for subsequent research (Engels, 1979). In an elegant series of experiments, Engels was able to show that hybrid dysgenesis could be explained by the interaction of polygenic chromosomal factors that appeared to be inherited in a Mendelian fashion, and a maternally inherited cytoplasmic state that he called ‘cytotype’. He proposed that the cytotype of M strain females is permissive for the activity of the chromosomal factors, P factors, which, in dysgenic flies, would be inherited from P strain males. The cytotype of a P strain would be non-permissive, thus accounting for the non-reciprocal nature of hybrid dysgenesis. He further suggested that P cytotype is determined by P factors themselves, explaining why P strains are genetically stable. Finally, he proposed that P factors might be transposable elements, as was thought to be the case for chromosomal factors responsible for a second form of hybrid dysgenesis, I–R hybrid dysgenesis (Picard, 1976). The suggestion that the chromosomal determinants responsible for P–M hybrid dysgenesis are transposable elements was confirmed by the identification of insertions of repeated sequences in the white gene in white-eye mutations isolated from the progeny of P–M dysgenic flies (Rubin et al., 1982). These insertions appeared to be deletion derivatives of a longer element, probably the P factor itself. This was cloned and shown to have P factor activity by injection into M strain embryos, an experiment","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"38 1","pages":"405-6"},"PeriodicalIF":0.0,"publicationDate":"2007-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77719417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Genetic variability and neutral mutations: a commentary on 'Genetic variability maintained in a finite population due to mutational production of neutral and nearly neutral isoalleles' by Motoo Kimura. 遗传变异和中性突变:Motoo Kimura对“由于中性和近中性等等位基因的突变产生而在有限种群中保持遗传变异”的评论。

Genetical research Pub Date : 2007-12-01 DOI: 10.1017/S001667230800952X

D. Gessler

引用次数: 0

Identity and coalescence in structured populations: a commentary on 'Inbreeding coefficients and coalescence times' by Montgomery Slatkin. 结构种群的同一性和合并:对Montgomery Slatkin的“近亲繁殖系数和合并时间”的评论。

Genetical research Pub Date : 2007-12-01 DOI: 10.1017/S0016672308009683

N. Barton

引用次数: 3

A model in two acts: a commentary on 'A model detectable alleles in a finite population' by Timoko Ohta and Motoo Kimura. 两种行为的模型:对Timoko Ohta和Motoo Kimura的“有限种群中可检测的等位基因模型”的评论。

Genetical research Pub Date : 2007-12-01 DOI: 10.1017/S0016672308009543

J. Hey

{"title":"A model in two acts: a commentary on 'A model detectable alleles in a finite population' by Timoko Ohta and Motoo Kimura.","authors":"J. Hey","doi":"10.1017/S0016672308009543","DOIUrl":"https://doi.org/10.1017/S0016672308009543","url":null,"abstract":"In the early 1970s, protein electrophoresis was the primary tool geneticists used to discover and measure allelic variation in natural populations. It was a relatively simple and inexpensive technique and, most importantly, it permitted the detection of multiple alleles regardless of polymorphism levels. This was a critical point because before the age of protein electrophoresis, segregating alleles were usually discovered only in cases where clearly discrete patterns of phenotypic variation were first observed. With protein electrophoresis a geneticist’s ability to identify multiple alleles did not depend on a prior indication of the presence of genetic variation (Hubby & Lewontin, 1966; Lewontin, 1974). The purpose of the short paper that Tomoko Ohta and her mentor Motoo Kimura published in Genetical Research in 1973 was to devise a mutation model that was explicitly appropriate for protein electrophoretic data and that would permit such data to be analysed with regard to questions on the relative roles of natural selection and genetic drift. As data on electrophoretic alleles began to accumulate, it was discovered that individuals were heterozygous, and many species were polymorphic, at a substantial fraction of the proteins that could be surveyed. These numbers on heterozygosity and polymorphism immediately began to feed a long-standing hunger, that had built up from decades of sophisticated modelling, for data on such topics as mutation rates, genetic load, the rate of neutral mutations, and the relative roles of natural selection and genetic drift in shaping levels and patterns of variation. Ohta and Kimura were the primary theoreticians of the neutral theory of molecular evolution and they had a very strong interest (as did most population geneticists of that age) in understanding how well the neutral theory explained the levels of polymorphism discovered by electrophoresis. The models they developed focused on amounts and patterns of genetic variation, and they tended to include explicitly a neutral mutation rate as well as assumptions about the nature of the mutation process. One prediction of the neutral theory was that the number of alleles in a population was expected to co-vary strongly with the effective population size. Earlier in 1964, Kimura and James Crow had developed the infinite alleles model, in which every mutation gives rise to a new allele (Kimura & Crow, 1964), and under this model the number of neutral alleles varies linearly with both effective population size and neutral mutation rate. Ohta and Kimura’s key idea in 1973 was a mutation model that explicitly gave rise to new allelic states in single steps that differed in net protein charge. Because four of the amino acids are normally charged at physiological pH, the surface of a soluble protein will carry a charge that affects its behaviour in gel electrophoresis, and mutations that raise or lower this charge will increase or decrease the rate of electrophoresis. In O","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"116 1","pages":"365-6"},"PeriodicalIF":0.0,"publicationDate":"2007-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79773891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Estimating the recombination parameter: a commentary on 'Estimating the recombination parameter of a finite population model without selection' by Richard R. Hudson. 重组参数的估计:对Richard R. Hudson“估计无选择的有限种群模型的重组参数”的评注。

Genetical research Pub Date : 2007-12-01 DOI: 10.1017/S0016672308009622

B. Weir

{"title":"Estimating the recombination parameter: a commentary on 'Estimating the recombination parameter of a finite population model without selection' by Richard R. Hudson.","authors":"B. Weir","doi":"10.1017/S0016672308009622","DOIUrl":"https://doi.org/10.1017/S0016672308009622","url":null,"abstract":"In 1987, Hudson proposed an estimator for the scaled recombination parameter C=4Nc, where N is the population size and c is the recombination rate between the two most distant of a set of segregating sites. This work came shortly after Kreitman (1983) published the first set of population genetic data at the DNA sequence level. Kreitman had been able to sequence 2.7 kilobases of the Drosophila melanogaster genome in 11 samples. It was felt at that time that population genetics was entering a new era, although Hudson cautioned that sufficiently large data sets for his new estimator ‘may require prohibitively large research efforts ’. Hudson’s estimator is based on the variance of the number of site differences between pairs of haplotypes and an estimate of the scaled mutation rate h=4Nm. The variance of the number of differences had already been shown by Brown et al. (1980) to be a convenient single-statistic summary of all the pairwise linkage disequilibria among a set of loci. The need for such a statistic continues as there is still doubt as to how well two-locus associations capture the full multilocus structure. Hudson provided an elegant derivation of the expected value of his statistic as a function of the unknown value C. His method of moments approach to estimation has the great virtue of simplicity although it would not be expected to behave as well as the maximum-likelihood methods that he (Hudson, 1993) and others (e.g. Kuhner et al., 2000; Wall, 2000; Fearnhead and Donnelly, 2001) developed later. Likelihood methods exploit all the information in a data set rather than just the information in a summary statistic and will do well provided the underlying evolutionary model is appropriate for the data being addressed. Writing 10 years after Hudson, Wakeley kept the same moment approach but provided modifications to Hudson’s method that improved its performance. Since 1983 the human genome has been sequenced, as have the genomes of several other species. There is now a ‘1000 genomes’ project (http://www.1000 genomes.org) under way for humans, and new sequencing techniques will make it possible very soon for population geneticists to obtain large samples of DNA sequence data. In 1987, Hudsonwished formore extensive DNA sequence data but he could not have foreseen the remarkable explosion of intermediate data – single-nucleotide polymorphisms (SNPs). Human geneticists are now generating 1 million SNP profiles for samples of thousands of individuals. By 2002, Hudson had produced a simulation procedure for SNP data (Hudson, 2002), and this has been used in studies such as Li and Stephens (2003) to detect recombination rate ‘hotspots ’. Hudson’s 1987 paper has the hallmarks of a classic paper. It introduced a new and simple method for estimating recombination rates from population samples rather than from pedigree data. More sophisticated methods have since been introduced, including composite-likelihood (Hudson, 2001) and others reviewed by H","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"20 1","pages":"425-6"},"PeriodicalIF":0.0,"publicationDate":"2007-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82373357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1